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waxMorph waxMorph
  • Installation
  • Tutorials
    • Forward simulator
    • Learned emulator (PyTorch)
    • Learned emulator (JAX)
  • Gallery
  • How-to guides
    • Train the emulator from meshes
    • Supervise multiple target frames
    • Choose a learning backend
    • Render trajectories
    • Running forward simulations: the epithelial-mesenchymal case study
  • Explanation
    • Cells as spheroidal agents
    • Forward and inverse modes
    • Graphs and locality
    • Emulator differentiability
    • Shape losses
    • Architecture
    • ADR 0001: Runtime and numerical contracts
  • Reference
    • Training APIs
      • waxmorph.train
        • waxmorph.train.TrainConfig
        • waxmorph.train.TrainResult
        • waxmorph.train.train
      • waxmorph.torch.train
        • waxmorph.torch.train.TrainConfig
        • waxmorph.torch.train.TrainResult
        • waxmorph.torch.train.train
      • waxmorph.jax.train
        • waxmorph.jax.train.TrainConfig
        • waxmorph.jax.train.TrainResult
        • waxmorph.jax.train.train
    • External API references
    • waxmorph
      • waxmorph.constants
      • waxmorph.data
        • waxmorph.data.load_mesh
        • waxmorph.data.normalize_mesh
        • waxmorph.data.sample_mesh_pair
        • waxmorph.data.sample_mesh_sequence
        • waxmorph.data.sample_volume
      • waxmorph.emulator
        • waxmorph.emulator.diffusion_step_differentiable
        • waxmorph.emulator.mech_step_sticky_differentiable
      • waxmorph.gnn
      • waxmorph.graph
      • waxmorph.jax
        • waxmorph.jax.gnn
        • waxmorph.jax.graph
        • waxmorph.jax.losses
        • waxmorph.jax.mlp
        • waxmorph.jax.warp_autograd
      • waxmorph.losses
      • waxmorph.mlp
      • waxmorph.render
        • waxmorph.render.MPLInterface
        • waxmorph.render.PyVistaInterface
        • waxmorph.render.RenderInterface
        • waxmorph.render.WarpMovieRenderer
      • waxmorph.simulator
        • waxmorph.simulator.chem_step
        • waxmorph.simulator.count_neighbors_step
        • waxmorph.simulator.gen_key_array
        • waxmorph.simulator.growth_step
        • waxmorph.simulator.mech_step_sticky
        • waxmorph.simulator.mech_step_sticky_implicit
      • waxmorph.torch
        • waxmorph.torch.gnn
        • waxmorph.torch.graph
        • waxmorph.torch.losses
        • waxmorph.torch.mlp
        • waxmorph.torch.warp_autograd
  • Contributing
  • Changelog
  • References
  • .rst

Explanation

Explanation#

These pages explain how waxMorph models a tissue and why it makes the choices it does. For specific tasks, see the How-to guides; for the API, see the Reference.

  • Cells as spheroidal agents
  • Forward and inverse modes
  • Graphs and locality
  • Emulator differentiability
  • Simulator derivative implementations
  • Shape losses
  • Architecture
  • ADR 0001: Runtime and numerical contracts

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Running forward simulations: the epithelial-mesenchymal case study

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Cells as spheroidal agents

By waxMorph Contributors

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